Microfluidic electrochemical system precisely manipulate fluid flow in microstructure to generate and transform energy. Among various microfluidic devices, microfluidic biofuel cells combine the microfluidic technology with bio-catalysts (e.g. enzyme, bacteria) and represent a novel carbon-neutral power generator. This paper gives a brief review of the recent accomplishments in microfluidic biofuel cells including fundamental working principles, state-of-the-art devices and key challenges. To be amenable to other micro systems, issues of energy output, scaling-up and functional-architecture design are especially proposed. The potential application opportunities in niche power source, sensor and analysis system are also discussed.